Generation updates

Autocorrelation graphs are generate now (which helps with debugging) and they are put in the space/mcmc dir.

progress_elapsed_time has been added as a new config option which defaults to 300 seconds (5 minutes)

Every progress_elapsed_time interval the system will write out the progress within the generation (percent complete, number of sims complete vs number of sims total). This is really helpful for slow generations with large populations to see how the system is progressing.